General information for g11454.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal recognition particle subunit SRP68.
Parent gene
- The parent gene g11454 is located on chr_1: 16355484..16357660 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g11454 | g11454.t3 | isoform | g11454.t3 | 16353269 | 16354371 |
| chr_1 | g11454 | g11454.t3 | exon | g11454.t3.exon1 | 16353269 | 16354371 |
| chr_1 | g11454 | g11454.t3 | cds | g11454.t3.CDS1 | 16353591 | 16354343 |
| chr_1 | g11454 | g11454.t3 | TSS | g11454.t3 | NA | NA |
| chr_1 | g11454 | g11454.t3 | TTS | g11454.t3 | NA | NA |
Sequences
>g11454.t3 Gene=g11454 Length=1103
ATCAAATCAAGAAGGACAATTATCTGGAATGCAATTTTTGCTCTCATACATACAGTACAT
TCGAATGAAATTAACACTTGAACGAAATTTATATTTGATTGGACAATTGAAACAAAACAA
AGAAGACGATGGTACGACGAAAAAAAGTCGTCCTCAAGACATTTCAAGATTATATGAGAT
AATTCTTCAAAATATAAGTGAAATGCAGCAACTAAATGGTCTTGAAAATGATACAGAGTA
TCAAAACGAAATAAAAGATTTAGCAAATGCTTTTAAAGCATTTAGATGTTACTATATTGC
TCTTACACTGGTTAATTTGAAACGTTGGAAAGAAGCTGTAGCAATGTATGAACGTTCAAC
AAAATATGCGACACAAGCGATCAAAGCAAAAGTCCACGAATTCAATTTACAAGCAGATCT
TAACGAATTGCTAAAAAACATTGAAGGAAATAAATTTTCCGCTCATGCTTATAGTGTTTT
AGAATCTGATAATCAAGATGAGACAGTCTTTTATGGTAAAACACAAAAAACTACTAAACC
TTTACTCGAGCGTCTCAATCAATACGTAGAGGATCCAACATTGAATTCAAAAAATCCTAA
TGTCTACAAATTAACTCCTGAAATGGAGGCTATTCCATGTAAACCTTTGTTTTTCGATTT
GGCTTTAAATTTTATCGAATTTCCATCGCTTGATGATAAGAAAGAACAAGTAACGAATAA
AAAAGTATCAGGAGTTGGAGGATTGATCAAAGGCTTCCTTGGTTTTGGAGATAAAAAATA
ATTTCTTTTTTGATTTATAGGTAAGTACTAACACTTATCATATGGAAGAAAATTTTACAT
CTTATTCTTTATATCGTATATATACGATTATTAAAAAAAGTTCATGTTTAATGCTAATTT
TTTTTTATCATTTTCAAATTGCATGCTCTTTTGAAAGAAAAACGTTGATATAGTTTCCTA
TGATGTTTAATAAAAATGCAAAAGTATGAACACATTAAAAAAATTGTTTACATTTTTAAT
CATCAGTATAGGATTATCTAAGAACACACACACATAATTTTCCTAATCGTGTTTAAAATA
AATAATTAGACAAACAAAATGCC
>g11454.t3 Gene=g11454 Length=250
MQFLLSYIQYIRMKLTLERNLYLIGQLKQNKEDDGTTKKSRPQDISRLYEIILQNISEMQ
QLNGLENDTEYQNEIKDLANAFKAFRCYYIALTLVNLKRWKEAVAMYERSTKYATQAIKA
KVHEFNLQADLNELLKNIEGNKFSAHAYSVLESDNQDETVFYGKTQKTTKPLLERLNQYV
EDPTLNSKNPNVYKLTPEMEAIPCKPLFFDLALNFIEFPSLDDKKEQVTNKKVSGVGGLI
KGFLGFGDKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g11454.t3 | PANTHER | PTHR12860 | SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN | 4 | 245 | 0 |
| 1 | g11454.t3 | Pfam | PF16969 | RNA-binding signal recognition particle 68 | 2 | 216 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006614 | SRP-dependent cotranslational protein targeting to membrane | BP |
| GO:0005786 | signal recognition particle, endoplasmic reticulum targeting | CC |
| GO:0030942 | endoplasmic reticulum signal peptide binding | MF |
| GO:0005047 | signal recognition particle binding | MF |
| GO:0008312 | 7S RNA binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
